Package: PrecisionTrialDrawer

Version: 0.99.17

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrecisionTrialDrawer_0.99.17.tar.gz

StartedAt: 2019-04-09 02:58:33 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:01:41 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 187.7 seconds

RetCode: 0

Status:  OK

CheckDir: PrecisionTrialDrawer.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrecisionTrialDrawer_0.99.17.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PrecisionTrialDrawer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PrecisionTrialDrawer’ version ‘0.99.17’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PrecisionTrialDrawer’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
panelDesigner  0.592  0.031   8.084
newCancerPanel 0.569  0.038   8.726
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PrecisionTrialDrawer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PrecisionTrialDrawer’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
* DONE (PrecisionTrialDrawer)

name	user	system	elapsed
CancerPanel-class	0.001	0.001	0.002
PrecisionTrialDrawer-package	0.266	0.011	0.276
appendRepo	1.060	0.034	1.096
coocMutexPlot	2.182	0.059	2.253
coveragePlot	0.303	0.016	0.320
coverageStackPlot	0.314	0.024	0.341
cpArguments	0.020	0.005	0.024
cpData	0.032	0.005	0.037
cpDataSubset	0.010	0.003	0.012
cpDesign	0.034	0.004	0.038
cpFreq	0.314	0.036	0.351
cpObj	0.277	0.009	0.286
cpObj2	0.068	0.006	0.074
dataExtractor	0.498	0.007	0.506
filterFusions	0.862	0.031	0.897
filterMutations	1.142	0.039	1.184
getAlterations	0.139	0.016	3.572
newCancerPanel	0.569	0.038	8.726
panelDesigner	0.592	0.031	8.084
panelOptimizer	0.001	0.001	0.001
panelexample	0.006	0.001	0.007
propPowerSampleSize	1.125	0.023	1.152
saturationPlot	1.933	0.073	2.013
showCancerStudy	0.009	0.001	0.248
showTumorType	0.040	0.002	0.271
subsetAlterations	0.728	0.030	0.759
survPowerSampleSize	0.904	0.010	0.922
survPowerSampleSize1Arm	0.930	0.015	0.949